[phenixbb] Problem with anomalous scattering factor refinement

[Nathaniel Echols]

This is an error in map calculation - I have a few suspicions about
what is breaking but I need to see what's happening internally.  Can
you please send me the logfile?

thanks,
Nat

On Wed, Dec 26, 2012 at 1:56 PM, Subhani Bandara <ramssb17 at gmail.com> wrote:
> Hi all,
>
> I've been trying to refine a structure with anomalous data with anomalous
> scattering factors. After some refinements without anomalous scattering
> factor refinement, I used the data.mtz file and original reflection file in
> reflection file editor to get the anomalous data merged with Rfree flags.
> When I tried to use this file with a pdb file (deleted hexadigest remark)
> and a cif file for ligands, the refinement ends with the following error at
> the end of the 3rd refinement cycle (I have only 3 cycles for a refinement).
>
> I was able to run a similar refinement with anomalous scattering factors for
> another structure without a problem. One difference in this structure is
> that this has NCS and the previous one didn't. I am using dev-1243 GUI.
>
> RuntimeError : scitbx array_family range error
>
> Traceback:
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/thread_utils.py",
> line 234, in run
>
>     return_value = self._target(self._args, self._kwargs, self._c)
>
>
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/runtime_utils.py",
> line 87, in __call__
>
>     result = self.target()
>
>
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/libtbx/runtime_utils.py",
> line 66, in __call__
>
>     result = self.run()
>
>
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/runtime.py",
> line 69, in run
>
>     refine_object = self._run(args, callback)
>
>
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/runtime.py",
> line 85, in _run
>
>     call_back_handler=callback)
>
>
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/command_line.py",
> line 169, in run
>
>     map_manger.write_files()
>
>
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/driver.py",
> line 1735, in write_files
>
>     map_coeff_dataset=self.write_mtz_file(),
>
>
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/phenix/phenix/refinement/driver.py",
> line 1724, in write_mtz_file
>
>     pdb_hierarchy=self.refine_object.model.pdb_hierarchy())
>
>
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/maps/__init__.py",
> line 500, in __init__
>
>     pdb_hierarchy = pdb_hierarchy)
>
>
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/maps/__init__.py",
> line 428, in map_coefficients_from_fmodel
>
>     sharp      = params.sharpening).map_coeffs
>
>
>
>   File
> "/Applications/PHENIX-dev-1243/Contents/phenix-dev-1243/cctbx_project/mmtbx/map_tools.py",
> line 55, in __init__
>
>     data = self.map_coeffs.data()*scale)
>
>
>
>
>
> Thanks in advance for any help
>
>
> Subhani
>
>
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